# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 19:51:48 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: (R)-[(1R)-1-amino-3-(methylsulfanyl)propyl]phosphinic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCC[C@H](N)[P@@H](O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 MPJ  MPJ  '(R)-[(1R)-1-amino-3-(methylsulfanyl)propyl]phosphinic acid'  L-peptide  20  9  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MPJ
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 MPJ  N    N  NH2    0  -0.796  1.1057   1.2833  -2.0711
 MPJ  CA   C  CH1    0  -0.327  1.7785   0.9305  -0.8266
 MPJ  CB   C  CH2    0  -0.444  1.1768  -0.3054  -0.1453
 MPJ  CG   C  CH2    0  -0.545  1.7094  -0.5762   1.2546
 MPJ  SD   S  S2     0  -0.057  0.7538  -1.9219   2.0138
 MPJ  CE   C  CH3    0  -0.762  1.6104  -2.0665   3.5967
 MPJ  P    P  P      0   0.968  3.5694   0.7224  -1.2336
 MPJ  H    H  HNH2   0   0.333  1.2035   0.5162  -2.7262
 MPJ  HN2  H  HNH2   0   0.341  0.1109   1.3847  -1.9058
 MPJ  HA   H  HCH1   0   0.225  1.6937   1.7844  -0.1439
 MPJ  HB1  H  HCH2   0   0.225  1.3401  -1.1800  -0.7830
 MPJ  HB2  H  HCH2   0   0.229  0.0921  -0.1597  -0.0915
 MPJ  HG1  H  HCH2   0   0.247  1.6189   0.3176   1.8767
 MPJ  HG2  H  HCH2   0   0.263  2.7617  -0.8539   1.2272
 MPJ  HE1  H  HCH3   0   0.258  1.5433  -1.1418   4.1687
 MPJ  HE2  H  HCH3   0   0.258  2.6590  -2.3267   3.4562
 MPJ  HE3  H  HCH3   0   0.270  1.1284  -2.8605   4.1645
 MPJ  HP   H  H      0  -0.055  3.8108   1.9848  -1.8683
 MPJ  O1   O  O      0  -0.821  3.6764  -0.3754  -2.2733
 MPJ  O2   O  OP    -1  -0.810  4.4110   0.6444   0.0231

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 MPJ  N   CA   single  1.458  0.019  1.458
 MPJ  N   H    single  0.860  0.020  0.860
 MPJ  N   HN2  single  0.868  0.020  1.013
 MPJ  CA  CB   single  1.521  0.033  1.521
 MPJ  CA  P    single  1.848  0.020  1.848
 MPJ  CA  HA   single  0.970  0.020  0.970
 MPJ  CB  CG   single  1.522  0.020  1.522
 MPJ  CB  HB1  single  0.939  0.020  1.096
 MPJ  CB  HB2  single  0.939  0.020  1.096
 MPJ  CG  SD   single  1.817  0.020  1.817
 MPJ  CG  HG1  single  0.939  0.020  1.096
 MPJ  CG  HG2  single  0.939  0.020  1.096
 MPJ  SD  CE   single  1.806  0.020  1.806
 MPJ  CE  HE1  single  0.939  0.020  1.096
 MPJ  CE  HE2  single  0.939  0.020  1.096
 MPJ  CE  HE3  single  0.939  0.020  1.096
 MPJ  O1  P    deloc   1.516  0.020  1.516
 MPJ  O2  P    deloc   1.514  0.020  1.514
 MPJ  P   HP   single  1.209  0.020  1.412

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 MPJ  HN2  N   H    106.02  3.000
 MPJ  HN2  N   CA   109.75  3.000
 MPJ  H    N   CA   114.00  3.000
 MPJ  HA   CA  P    107.44  3.000
 MPJ  HA   CA  CB   109.00  3.000
 MPJ  P    CA  CB   112.77  3.000
 MPJ  HA   CA  N    110.00  3.000
 MPJ  P    CA  N    106.64  3.000
 MPJ  CB   CA  N    110.40  1.500
 MPJ  HB2  CB  HB1  106.41  3.000
 MPJ  HB2  CB  CG   108.96  3.000
 MPJ  HB1  CB  CG   109.96  3.000
 MPJ  HB2  CB  CA   107.63  3.000
 MPJ  HB1  CB  CA   109.06  3.000
 MPJ  CG   CB  CA   114.49  3.000
 MPJ  HG2  CG  HG1  107.64  3.000
 MPJ  HG2  CG  SD   109.27  3.000
 MPJ  HG1  CG  SD   108.93  3.000
 MPJ  HG2  CG  CB   111.13  3.000
 MPJ  HG1  CG  CB   110.43  3.000
 MPJ  SD   CG  CB   109.40  3.000
 MPJ  CE   SD  CG   100.14  3.000
 MPJ  HE3  CE  HE2  108.62  3.000
 MPJ  HE3  CE  HE1  108.54  3.000
 MPJ  HE2  CE  HE1  109.25  3.000
 MPJ  HE3  CE  SD   107.79  3.000
 MPJ  HE2  CE  SD   111.26  3.000
 MPJ  HE1  CE  SD   111.29  3.000
 MPJ  HP   P   O2   108.61  3.000
 MPJ  HP   P   O1   108.80  3.000
 MPJ  O2   P   O1   119.52  3.000
 MPJ  HP   P   CA    99.29  3.000
 MPJ  O2   P   CA   111.19  3.000
 MPJ  O1   P   CA   107.52  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 MPJ  Var_01  SD   CG  CB  CA  172.45  30.0  3
 MPJ  Var_02  HE1  CE  SD  CG   61.27  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 MPJ  chir_01  CA  N  CB  P  negativ

